From mgiglio at som.umaryland.edu Tue Apr 1 14:18:23 2008 From: mgiglio at som.umaryland.edu (Gwinn Giglio, Michelle) Date: Tue, 01 Apr 2008 17:18:23 -0400 Subject: [gofriends] New subcodes of ISS are now available Message-ID: Hello GO Friends, As announced in the February 2008 GO newsletter, the GO Consortium has added three new subcodes for the ISS (Inferred from Sequence or Structural Similarity) evidence code. These go into effect today. These codes have been created to clarify the type of sequence-based methods used as evidence in making annotations. The new codes are: Inferred from Sequence Alignment (ISA), Inferred from Sequence Orthology (ISO), and Inferred from Sequence Model (ISM). Detailed documentation describing each of these codes is now available on the GO Evidence Code page: http://www.geneontology.org/GO.evidence.shtml Some brief descriptions of the new codes: ISA should be used when an annotation is based on pairwise or multiple alignments of the query protein with experimentally characterized proteins. Examples of tools that produce these types of alignments are BLAST, MUSCLE, and ClustalW. ISO should be used when a protein is determined to be orthologous with an experimentally characterized protein from another species. Orthologous genes share a common ancestor and have arisen due to a speciation event. Orthologs are determined from phylogenetic analysis using algorithms such as maximum likelihood or nearest neighbor joining. ISM indicates use of a statistical modeling tool to determine a protein?s membership in a particular functional family, or to predict the presence of a particular sequence domain or structure. Examples of ISM evidence types are Hidden Markov Models (HMMs), tRNAscan, and transmembrane-HMM (TMHMM). Many thanks to everyone on the Evidence Committee for their work on writing the new documentation and getting it up onto the web page. Please let us know if you have any questions. Michelle (and the rest of the Evidence Committee) -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From dbarrell at ebi.ac.uk Wed Apr 2 09:03:23 2008 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Wed, 02 Apr 2008 17:03:23 +0100 Subject: [Gofriends] April 2008 GOA release In-Reply-To: <42690FC8.8010409@ebi.ac.uk> References: <42690FC8.8010409@ebi.ac.uk> Message-ID: <47F3AE4B.5080204@ebi.ac.uk> GOA releases: April 2008 ============================ GOA (GO Annotation at EBI) is a project run by the European Bioinformatics Institute that aims to provide assignments of gene products to the Gene Ontology (GO) resource. The data can be obtained via: EBI FTP: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/ EBI SRS: http://srs.ebi.ac.uk. Search GOA data library GO FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/ GO CVS: http://www.geneontology.org/GO.CVS.help.html (the last two will be updated overnight) For further information read: http://www.ebi.ac.uk/GOA or contact goa at ebi.ac.uk. The GOA group has started to produce, in collaboration with the British Heart Foundation-funded Cardiovascular Gene Ontology Annotation Initiative, a BHF-UCL gene association file, which contains all GO annotations for 4,027 human proteins implicated in cardiovascular development or disease. The BHF-UCL file is a sub-set of the UniProt gene association file, and will provide the cardiovascular community with a discrete set of relevant GO annotations. This file will be updated by GOA monthly and can be downloaded from: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/bhf-ucl/gene_association.goa_bhf-ucl.gz The University College London based Gene Ontology Annotation Initiative aims to prioritise the manual annotation of genes associated with the cardiovascular system, for further information on this project, please see: http://www.ucl.ac.uk/medicine/cardiovascular-genetics/geneontology.html http://wiki.geneontology.org/index.php/Cardiovascular_Gene_Page Regards The UniProt GOA Team From Sophie.DERET at galderma.com Fri Apr 4 00:23:04 2008 From: Sophie.DERET at galderma.com (DERET Sophie) Date: Fri, 4 Apr 2008 09:23:04 +0200 Subject: [Gofriends] GO tools Message-ID: <9C2081B5FF465A4BB637BE293A8A00C208041276@frncemsx01.sd.galderma.com> Dear all, Do you know of any GO tool that allows you to visualise simultaneously the GO annotations of several gene lists (on the same DAG view) ? Thanks a lot. Sophie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20080404/bb57fee9/attachment.html From goetz_stefan at gmx.de Sat Apr 5 06:51:41 2008 From: goetz_stefan at gmx.de (Stefan Goetz) Date: Sat, 05 Apr 2008 15:51:41 +0200 Subject: [Gofriends] GO tools In-Reply-To: <9C2081B5FF465A4BB637BE293A8A00C208041276@frncemsx01.sd.galderma.com> References: <9C2081B5FF465A4BB637BE293A8A00C208041276@frncemsx01.sd.galderma.com> Message-ID: <47F783ED.3080406@gmx.de> Dear Sopie, please have a look at the GO-Graph-Viewer from the Babelomics suite at www.babelomics.org. "The DAG viewer tool generates joined gene ontology graphs (DAGs) to create overviews of the functional context of groups of sequences. Interactive graph visualization allows the navigation of large and unwieldy graphs often generated when trying to biologically explore large sets of sequence annotations. Zoom and graph navigation is provided through the DAG viewer Java Web Start tool." You can find a tutorial here: http://bioinfo.cipf.es/babelomicswiki/doku.php?id=tool:gographviz If your need any further support or help just contact us again! Best regards, Stefan Goetz -------------------------------------------- Stefan G?tz Bioinformatics Department Centro de Investigaci?n Pr?ncipe Felipe (CIPF) C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanogr?fico) 46013 Valencia, Spain Tel: +34 963289680 Ext. 1011 Fax: +34 963289574 E-Mail: sgoetz at cipf.es http://bioinfo.cipf.es -------------------------------------------- DERET Sophie wrote: > > Dear all, > > Do you know** ****of*** *any GO tool that allows you to visualise > _simultaneously_ the GO > > annotations of _several_ gene lists (on the same DAG view) ? > > Thanks a lot. > > Sophie > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Gofriends mailing list > Gofriends at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/gofriends > From phillip.lord at newcastle.ac.uk Mon Apr 14 05:31:59 2008 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Mon, 14 Apr 2008 13:31:59 +0100 Subject: [Gofriends] CFP: Bio-Ontologies 2008: Knowledge in Biology Message-ID: <87skxohb28.fsf@dinley.ncl.ac.uk> ** Call for Papers Submissions are now invited Bio-Ontologies 2008: Knowledge in Biology, a SIG at Intelligent Systems for Molecular Biology 2008. *** Key Dates - Submission due: **Friday 2nd May** - Notifications: **Friday 23rd May** - Final Version Due: **Friday 30th May** - Workshop: **Sunday 20th July** *** Introduction Bio-Ontologies has existed as a SIG at ISMB (http://www.iscb.org/ismb2008) for more than a decade, making it one of the longest running. For this time, Bio-Ontologies has provided a forum for discussion on the latest and most cutting edge research on ontologies. In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. Following on from last year's reflective look, this year we are broadening the scope of SIG; we are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology. So, for example: - Semantic and/or Scientific wikis. - Multimedia blogs - Folksonomies - Tag Clouds - Collaborative Curation Platforms - Collaborative Ontology Authoring and Peer-Review Mechanisms are topics which will be of relevance to the SIG, in addition to the more traditional areas for bio-ontologies. - Biological Applications of Ontologies - Reports on Newly Developed or Existing Bio-Ontologies - Tools for Developing Ontologies - Use of Ontologies in Data Communication Standards - Use of Semantic Web technologies in Bioinformatics - Implications of Bio-Ontologies or the Semantic Web for drug discovery - Current Research In Ontology Languages and its implication for Bio-Ontologies Please note, that this year ISCB have made an innovative schedule, holding some of the SIGs **DURING** ISMB. Bio-Ontologies is on the Sunday parallel to the main conference. ** Programme This year's keynote speaker will be Professor **Philip E. Bourne**, from the Skaggs School of Pharmacy & Pharmaceutical Sciences, UCSD. Our panel session will the following members: - Philip E. Bourne, UCSD - Helen Parkinson, European Bioinformatics Institute - Matt Cockerill, BioMed Central - Mark Wilkinson, University of British Columbia *** Submissions Submissions are now open and can be submitted through easychair (http://www.easychair.org/conferences/?conf=bioontologies2008). *** Instructions to Authors We are inviting two types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1/2 page. Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the day for at least one poster session. Unsuccesful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic. The best papers from Bio-Ontologies 2008: Knowledge in Biology will be published in BMC Bioinformatics. *** Organisers Phillip Lord, Newcastle University Susanna-Assunta Sansone, EBI Nigam Shah, Stanford Matt Cockerill, BioMedCentral *** Programme Committee The programme committee, organised alphabetically is: Mike Bada, University of Colorado Judith Blake, Jackson Laboratory Frank Gibson, Newcastle University Cliff Joslyn, Pacific National Laboratory Wacek Kusnierczyk, Norwegian University of Science and Technology Robin MacEntire, GSK Helen Parkinson, EBI Daniel Rubin, Stanford University Alan Ruttenberg, Science Commons Susie M. Stephens, Eli Lilly Robert Stevens, University of Manchester and the conference organisers. *** Templates Submission templates are available from the website (http://bio-ontologies.org.uk). -- Phillip Lord, Phone: +44 (0) 191 222 7827 Lecturer in Bioinformatics, Email: phillip.lord at newcastle.ac.uk School of Computing Science, http://homepages.cs.ncl.ac.uk/phillip.lord Claremont Tower Room 909, skype: russet_apples Newcastle University, msn: msn at russet.org.uk NE1 7RU From midori at ebi.ac.uk Thu Apr 24 05:22:47 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 24 Apr 2008 13:22:47 +0100 (BST) Subject: [Gofriends] GO SourceForge tracker cleanup Message-ID: Dear Colleagues, As you may know, the GO Consortium uses a tracker at the SourceForge site to log requests for new terms and other changes in the ontology content and structure. The tracker is here: https://sourceforge.net/tracker/?atid=440764&group_id=36855&func=browse Because we have a large backlog of requests, we have decided to close a large number of items that were opened a long time ago, and are therefore likely to be out of date. This will help us set priorities for our work, as well as reducing the number of open tracker items. On May 12, 2008 we will close all items that meet both of these criteria: - open for more than one year (i.e. opened before May 12, 2007) - not assigned to a GO curator Any item can be reopened if we receive any comments (via the SourceForge tracker, email, or any other mode of communication) indicating that it is still of interest to the original submitter or another party. Please let us know if you have any comments or questions; you can reach the GO Consortium via the GO helpdesk email . Sincerely, Midori Harris on behalf of the GO ontology developers ============================ Midori A. Harris, Ph.D. GO Editor EMBL - EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 (0) 1223 494667 Fax: +44 (0) 1223 494468 Email: midori at ebi.ac.uk From darin.london at duke.edu Tue Apr 29 10:00:36 2008 From: darin.london at duke.edu (darin.london at duke.edu) Date: Tue, 29 Apr 2008 13:00:36 -0400 Subject: [Gofriends] BOSC 2008 Announcement and Call For Submissions Message-ID: <200804291700.m3TH0aKQ020912@tenero.duhs.duke.edu> BOSC 2008 Call for Abstracts Reminder The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008). This is a reminder to submit your proposals for talks to the BOSC submission system before May 11. Submission Process: All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php). The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details) Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t Important Dates: May 11: Abstract submission deadline. June 2: Notification of accepted talks. June 4: Early registration discount cut-off. July 18-19: BOSC 2008! We hope to see you at BOSC 2008! Kam Dahlquist and Darin London BOSC 2008 Co-organizers